Hi Ann, Thanks for your response. I am using the website, not a mirror. I converted my files to MAF and it worked well.
The only thing left is cosmetic - I was wondering if it were possible to shade the background a different color. Also, I noticed the MAF file can include a quality score, but I can't figure out how the quality score affects the output (like changing the color or something). If I were to use a mirror, would I have more control in manipulating such things? Thanks, Jeremy On Tue, Jan 6, 2009 at 11:50 AM, Ann Zweig <[email protected]> wrote: > Hi Jeremy, > > If you are running a mirror of our genome browser, then you should be able > to create such a track. If that's the case, let us know and we can give you > more detailed instruction. Here's the information about creating a mirror: > http://genome.ucsc.edu/admin/mirror.html > > The Genome Browser and Blat software are free for academic, nonprofit, and > personal use. A license is required for commercial use. > > If you are, instead, trying to do this using our website and source code > tools, I cam give you some pointers to get that done. You will use two kent > source tools: pslPretty and axtToMaf. In general (for PSL -> MAF > translation): > > pslPretty -axt | axtToMaf > > See this previously-answered mail list question for more details: > http://www.soe.ucsc.edu/pipermail/genome/2008-November/017574.html > > You may have to make a few edits to the resulting MAF file in order to > display it as a Custom Track. Read more about creating a MAF Custom Track > here: http://genome.ucsc.edu/FAQ/FAQformat.html#format5 > > > I hope this information is helpful to you. Please don't hesitate to contact > the mail list again if you require further assistance. > > > Regards, > > ---------- > Ann Zweig > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > > > > > Jeremy Davis-Turak wrote: >> >> Hi, >> >> I'm trying to create a track of aligned Illumina sequencing reads. >> Currently I am using a .BED file, but I am having trouble with >> displaying the mismatches in those alignments. I would like to have >> them look just like the BLAT alignment results, where mismatches have >> a changed base, and indels are shown. However, the PSLX format does >> not seem to be supported. I noticed that the BLAT results are a >> combination of a .FA file and and a .PSL file. Is there any support >> for creating combining these files, outside of using BLAT? >> >> Thanks, >> >> Jeremy >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
